Project description:We present PIGEON-FEATHER, a method for calculating free energies of opening (∆Gop) at single- or near-single-amino acid resolution for protein ensembles of all sizes from hydrogen exchange/mass spectrometry (HX/MS) data. PIGEON-FEATHER disambiguates and reconstructs all experimentally measured isotopic mass envelopes using a Bayesian Monte Carlo sampling approach. We applied PIGEON-FEATHER to reveal how E. coli and human dihydrofolate reductase (ecDHFR, hDHFR) have evolved distinct conformational ensembles tuned to their catalytic cycles. We showed how two competitive inhibitors of ecDHFR arrest its ensemble in different ways, only one of which is compatible with vertebrate DHFR orthologs. Finally, we uncovered how the lac repressor (LacI) ensemble responds to binding its inducer molecule and operator DNA to regulate transcriptional activation.
Project description:We present PIGEON-FEATHER, a method for calculating free energies of opening (∆Gop) at single- or near-single-amino acid resolution for protein ensembles of all sizes from hydrogen exchange/mass spectrometry (HX/MS) data. PIGEON-FEATHER disambiguates and reconstructs all experimentally measured isotopic mass envelopes using a Bayesian Monte Carlo sampling approach. We applied PIGEON-FEATHER to reveal how E. coli and human dihydrofolate reductase (ecDHFR, hDHFR) have evolved distinct conformational ensembles tuned to their catalytic cycles. We showed how two competitive inhibitors of ecDHFR arrest its ensemble in different ways, only one of which is compatible with vertebrate DHFR orthologs. Finally, we uncovered how the lac repressor (LacI) ensemble responds to binding its inducer molecule and operator DNA to regulate transcriptional activation.
Project description:A comparative profile of miRNAs in livers during pigeon development was performed by using high-throughput sequencing. We identified known pigeon miRNAs, novel miRNAs, and miRNAs that are conserved in other birds and mammals.Our results expanded the repertoire of pigeon miRNAs and may be of help in better understanding the mechanism of squab’s rapid development from the perspective of liver development.
Project description:A comparative profile of miRNAs in pectoral muscle during pigeon development was performed by using high-throughput sequencing. We identified known pigeon miRNAs, novel miRNAs, and miRNAs that are conserved in other birds and mammals.Our results expanded the repertoire of pigeon miRNAs and may be of help in better understanding the mechanism of squab’s rapid development.
Project description:Deep sequencing of mRNA from the rock pigeon Analysis of ploy(A)+ RNA of different specimens: heart and liver from the rock pigeon (Danish Tumbler, Oriental Frill and Racing)
